The long-term objective of this proposal is to conduct a NexGen RNA-Seq based dissection of the gene expression program driving kidney development. The central thesis is straightforward. We propose to define, in a sensitive and quantitative manner, all of the sets of genes active in each critical cell type of the developing kidney. An atlas will be generated, comprehensive in character, including microRNAs as well as more orthodox coding mRNAs, and providing detailed analyses of alternative RNA processing events. The end result will be an essential resource, describing the analog gene expression code that defines and drives each compartment of the developing kidney. This resource will identify all of the growth factors, receptors and transcription factors expressed in each cell type. It will establish a set of novel cell type specific molecular markers, useful in mutant analyses. In addition it will provide a standard baseline for the global analysis of changes in gene expression patterns occurring as a result of mutation or disease. In addition we propose to use a Chip-Seq approach to discover the direct downstream targets of the transcription factors Hoxa11, Lhx1 and Six2. Each has been shown to play an important role in kidney development, and by identifying their direct downstream targets we will gain a better view of their precise roles in the process of nephrogenesis. PUBLIC HEALTH RELEVANCE: The proposed work would use the latest revolutionary sequencing technology to characterize all of the gene activities in the many different cell types of the developing kidney. This would lead to a much deeper understanding of the genetic program that drives the process of making a kidney, which in turn will in time help us better understand how to repair kidneys that have been damaged by disease.